This run was generated using rMAP version 1.0 performed on 2021-09-01… Thank you for using this pipeline!!


Assembly summary statistics


Field Description
SampleID Name of the sample
TrimReads Total number of reads after quality filtering
MeanReadLen Average read length after quality filtering
Contigs Number of contigs of the draft genome (>200bp)
GenomeLength Length (bp) of the draft genome
LargestContig Length (bp) of the largest contig in the genome
N50 Length of the smallest contig in the set that contains the fewest (largest) contigs whose combined length represents at least 50% of the assembly
GC-Content GC content (%) of the draft genome
Depth Number of times each nucleotide position in the draft genome has a read that aligns to that position


SampleID TrimReads MeanReadLen Contigs GenomeLength LargestContig N50 GC-Content Depth
ID084I 355637 132 62 5074296 548642 225746 51.66 9X
ORTHO013EII 345294 133 2785 8669942 55924 5621 55.41 5X
ORTHO039E 433286 133 102 5004643 337885 124175 55.00 11X

Select the parameter

Number of reads

Average number of reads per sample = 378072

Average read length

Average read length per sample = 133 bp

Number of contigs

Average number of contigs per sample = 983

Genome length

Average genome length per sample = 6249627 bp

Largest contig length

Average largest contig length per sample = 314150 bp

N50

Average N50 per sample = 118514 bp

GC content

Average GC content per sample = 54.023%

Sequencing depth

Average sequencing depth = 8.333X

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SNP-variant calling


Field Description
GenomePosition Position in the genome where SNP is found
Type Nature of the SNP identified (Only ‘True’ SNPs are shown by default)
ReferenceAllele Allele found in the reference genome
AlternateAllele Allele found in the genome of interest forming the SNP
Consequence Amino acid alterations caused by the SNP
AffectedGene The tartget gene affected by the SNP
Product The outcome from the presence of the SNP


Select the sample

ID084I
GenomePosition Type ReferenceAllele AlternateAllele Consequence AffectedGene Product
1619514 snp A C missense_variant c.1014T>G p.His338Gln NA phage resistance protein
1680903 snp T C missense_variant c.406T>C p.Trp136Arg NA multidrug resistance outer membrane protein MdtQ
1681054 snp G A missense_variant c.557G>A p.Ser186Asn NA multidrug resistance outer membrane protein MdtQ
2153125 snp T C missense_variant c.44T>C p.Ile15Thr NA putative copper resistance protein CopD
2473709 snp G A missense_variant c.5G>A p.Ser2Asn NA tellurite resistance protein TehA
2473825 snp G A missense_variant c.121G>A p.Gly41Ser NA tellurite resistance protein TehA
2537962 snp C T missense_variant c.371C>T p.Ala124Val NA methyl viologen resistance protein SmvA
2538486 snp T G missense_variant c.895T>G p.Leu299Val NA methyl viologen resistance protein SmvA
2745862 snp A T missense_variant c.74A>T p.Gln25Leu NA fusaric acid resistance protein
2746092 snp G A missense_variant c.304G>A p.Val102Met NA fusaric acid resistance protein
2747688 snp G A missense_variant c.1900G>A p.Ala634Thr NA fusaric acid resistance protein
2747736 snp A G missense_variant c.1948A>G p.Ile650Val NA fusaric acid resistance protein
3068212 snp C T missense_variant c.284G>A p.Arg95Gln NA arsenic resistance operon repressor
3068294 snp G A missense_variant c.202C>T p.His68Tyr NA arsenic resistance operon repressor
3068389 snp G A missense_variant c.107C>T p.Ala36Val NA arsenic resistance operon repressor
3068804 snp A G missense_variant c.224A>G p.Asp75Gly NA arsenical resistance protein ArsH
3069242 snp A T missense_variant c.662A>T p.Gln221Leu NA arsenical resistance protein ArsH
3839989 snp A T missense_variant c.539A>T p.Glu180Val NA oxidative-stress-resistance chaperone
4708330 snp G A missense_variant c.646G>A p.Asp216Asn NA multidrug resistance efflux RND protein MdtN
4708574 snp A T missense_variant c.890A>T p.Gln297Leu NA multidrug resistance efflux RND protein MdtN
4709233 snp C T missense_variant c.518C>T p.Thr173Ile NA multidrug resistance efflux RND protein MdtO
4709280 snp G A missense_variant c.565G>A p.Ala189Thr NA multidrug resistance efflux RND protein MdtO
4709431 snp T C missense_variant c.716T>C p.Val239Ala NA multidrug resistance efflux RND protein MdtO
4709685 snp A G missense_variant c.970A>G p.Asn324Asp NA multidrug resistance efflux RND protein MdtO
4710312 snp A G missense_variant c.1597A>G p.Met533Val NA multidrug resistance efflux RND protein MdtO
4710422 snp A G missense_variant c.1707A>G p.Ile569Met NA multidrug resistance efflux RND protein MdtO
4710477 snp A G missense_variant c.1762A>G p.Thr588Ala NA multidrug resistance efflux RND protein MdtO
ORTHO013EII
GenomePosition Type ReferenceAllele AlternateAllele Consequence AffectedGene Product
4579070 snp G C missense_variant c.639C>G p.Ile213Met NA tellurium resistance protein TerX
4579107 snp A T missense_variant c.602T>A p.Val201Glu NA tellurium resistance protein TerX
4579147 snp G C missense_variant c.562C>G p.Pro188Ala NA tellurium resistance protein TerX
4579656 snp A T missense_variant c.53T>A p.Phe18Tyr NA tellurium resistance protein TerX
4579877 snp T C missense_variant c.493A>G p.Thr165Ala NA tellerium resistance protein TerY
4579973 snp T C missense_variant c.397A>G p.Thr133Ala NA tellerium resistance protein TerY
4590524 snp A G missense_variant c.508A>G p.Thr170Ala NA tellurium resistance protein TerA
4590567 snp A C missense_variant c.551A>C p.Lys184Thr NA tellurium resistance protein TerA
4590680 snp A G missense_variant c.664A>G p.Ser222Gly NA tellurium resistance protein TerA
4590696 snp G C missense_variant c.680G>C p.Gly227Ala NA tellurium resistance protein TerA
4590800 snp G A missense_variant c.784G>A p.Asp262Asn NA tellurium resistance protein TerA
4592008 snp G A missense_variant c.334G>A p.Val112Ile NA tellurium resistance protein TerC
4592146 snp A G missense_variant c.472A>G p.Asn158Asp NA tellurium resistance protein TerC
4592642 snp C G missense_variant c.968C>G p.Ala323Gly NA tellurium resistance protein TerC
4592686 snp G A missense_variant c.1012G>A p.Glu338Lys NA tellurium resistance protein TerC
4592694 snp T A missense_variant c.1020T>A p.Asp340Glu NA tellurium resistance protein TerC
4592808 snp A G missense_variant c.46A>G p.Thr16Ala NA tellurium resistance protein TerD
4592967 snp G T missense_variant c.205G>T p.Ala69Ser NA tellurium resistance protein TerD
4593470 snp G A missense_variant c.64G>A p.Val22Ile NA chemical-damaging agent resistance protein C
4593519 snp G C missense_variant c.113G>C p.Gly38Ala NA chemical-damaging agent resistance protein C
4593745 snp A T missense_variant c.339A>T p.Glu113Asp NA chemical-damaging agent resistance protein C
5028187 snp C G missense_variant c.391C>G p.Leu131Val NA chloramphenical resistance permease RarD
ORTHO039E
GenomePosition Type ReferenceAllele AlternateAllele Consequence AffectedGene Product
2638763 snp A T missense_variant c.382A>T p.Thr128Ser NA multiple antibiotic resistance transcriptional regulator MarR
2638803 snp G A missense_variant c.422G>A p.Arg141Lys NA multiple antibiotic resistance transcriptional regulator MarR
2638892 snp A G missense_variant c.58A>G p.Asn20Asp NA multiple antibiotic resistance transcriptional regulator MarA
4579070 snp G C missense_variant c.639C>G p.Ile213Met NA tellurium resistance protein TerX
4579107 snp A T missense_variant c.602T>A p.Val201Glu NA tellurium resistance protein TerX
4579147 snp G C missense_variant c.562C>G p.Pro188Ala NA tellurium resistance protein TerX
4579656 snp A T missense_variant c.53T>A p.Phe18Tyr NA tellurium resistance protein TerX
4579877 snp T C missense_variant c.493A>G p.Thr165Ala NA tellerium resistance protein TerY
4579973 snp T C missense_variant c.397A>G p.Thr133Ala NA tellerium resistance protein TerY
4582643 snp A G missense_variant c.224T>C p.Ile75Thr NA tellurium resistance protein TerW
4582708 snp A C missense_variant c.159T>G p.Asp53Glu NA tellurium resistance protein TerW
4582779 snp C T missense_variant c.88G>A p.Ala30Thr NA tellurium resistance protein TerW
4590375 snp A G missense_variant c.359A>G p.Asn120Ser NA tellurium resistance protein TerA
4590524 snp A G missense_variant c.508A>G p.Thr170Ala NA tellurium resistance protein TerA
4590567 snp A C missense_variant c.551A>C p.Lys184Thr NA tellurium resistance protein TerA
4590680 snp A G missense_variant c.664A>G p.Ser222Gly NA tellurium resistance protein TerA
4590696 snp G C missense_variant c.680G>C p.Gly227Ala NA tellurium resistance protein TerA
4592008 snp G A missense_variant c.334G>A p.Val112Ile NA tellurium resistance protein TerC
4592146 snp A G missense_variant c.472A>G p.Asn158Asp NA tellurium resistance protein TerC
4592686 snp G A missense_variant c.1012G>A p.Glu338Lys NA tellurium resistance protein TerC
4592694 snp T A missense_variant c.1020T>A p.Asp340Glu NA tellurium resistance protein TerC
4592808 snp A G missense_variant c.46A>G p.Thr16Ala NA tellurium resistance protein TerD
4593745 snp A T missense_variant c.339A>T p.Glu113Asp NA chemical-damaging agent resistance protein C
5028013 snp A G missense_variant c.217A>G p.Ile73Val NA chloramphenical resistance permease RarD
5028139 snp G T missense_variant c.343G>T p.Val115Leu NA chloramphenical resistance permease RarD
5028187 snp C G missense_variant c.391C>G p.Leu131Val NA chloramphenical resistance permease RarD


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Phylogenetic inference

Phylogeny inference was not performed.


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Antimicrobial Resistance Profiling


Field Description
Contig Contig name where the gene was found
Start Start position of the gene within the contig
End End position of the gene within the contig
Gene Antibiotic resistance gene
Gaps Gaps in subject (genome) and query (antibiotic resistance gene)
Coverage Proportion (%) of the gene covered
Identity Proportion (%) of exact nucleotide matches
Accession Accesion number of the antibiotic resistance gene
Product Antibiotic resistance gene product
Resistance Antibiotic that the gene confers resistance to


Select the samples and the database

ID084I
Resfinder
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00041 3482 4081 aac(6’)-Ib-cr_1 0/0 100.0 100.0 DQ303918 aac(6’)-Ib-cr Ciprofloxacin
contig00041 1301 2146 aadA16_1 0/0 100.0 99.6 EU675686 aadA16 Streptomycin
contig00041 2933 3425 ARR-3_4 0/0 90.8 99.2 FM207631 ARR-3
contig00017 99900 101045 blaCMY-97_1 0/0 100.0 99.8 KC007363 blaCMY-97 Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefotaxime, Cefoxitin, Ceftazidime, Piperacillin, Piperacillin+Tazobactam, Ticarcillin, Ticarcillin+Clavulanic_acid
contig00035 3701 4576 blaCTX-M-15_1 0/0 100.0 100.0 AY044436 blaCTX-M-15 Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00035 19 879 blaTEM-1B_1 0/0 100.0 100.0 AY458016 blaTEM-1B Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00041 2327 2800 dfrA27_1 0/0 100.0 100.0 FJ459817 dfrA27 Trimethoprim
contig00046 192 836 qnrB6_2 0/0 100.0 100.0 EF523819 qnrB6 Ciprofloxacin
contig00041 4 870 sul1_5 0/0 100.0 99.9 EU780013 sul1 Sulfamethoxazole
contig00037 2675 3490 sul2_2 0/0 100.0 100.0 AY034138 sul2 Sulfamethoxazole
contig00035 7810 8994 tet(D)_1 0/0 100.0 99.9 AF467077 tet(D) Doxycycline, Tetracycline
CARD
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00041 3482 4081 AAC(6’)-Ib-cr 0/0 100 100.0 DQ303918:0-600 AAC(6’)-Ib-cr is an aminoglycoside acetyltransferase encoded by plasmids transposons integrons in Enterobacteriaceae. The aac(6’)-Ib-cr variant gene can induce resistance against aminoglycoside and fluoroquinolone simultaneously aminoglycoside, fluoroquinolone
contig00041 1301 2146 aadA16 0/0 100 99.6 EU675686:3196-4042 aadA16 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids and integrons in E. coli V. cholerae and K. pneumoniae aminoglycoside
contig00041 2933 3385 arr-3 0/0 100 100.0 EU675686:1956-2409 arr-3 is a plasmid-encoded ribosyltransferase found in Vibrio fluvialis rifamycin
contig00017 99900 101045 CMY-65 0/0 100 99.6 JF780936:63-1209 CMY-65 is a beta-lactamase. From the Lahey list of CMY beta-lactamases. cephamycin
contig00035 3701 4576 CTX-M-15 0/0 100 100.0 AY044436:1435-2311 CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family cephalosporin
contig00041 2327 2800 dfrA27 0/0 100 100.0 KP076293.1:2347-2821 A dihydrofolate reductase and trimethoprim resistance gene from non-O1 non-O139 Vibrio cholerae diaminopyrimidine
contig00002 419944 420357 H-NS 0/0 100 90.3 BA000007.3:1738104-1737690 H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters. cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00046 156 836 QnrB17 0/0 100 99.8 AM919398:0-681 QnrB17 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii fluoroquinolone
contig00041 4 843 sul1 0/0 100 100.0 JF969163:1053-1893 Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons. sulfonamide
contig00037 2675 3490 sul2 0/0 100 100.0 AY055428.1:21084-20268 Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids. sulfonamide
contig00035 19 879 TEM-1 0/0 100 99.9 AL513383:161910-162771 TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins. cephalosporin, monobactam, penam, penem
contig00035 7810 8994 tet(D) 0/0 100 99.9 AF467077.1:163-1348 TetD is a tetracycline efflux pump found exclusively in Gram-negative bacteria. tetracycline
ARG-ANNOT
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00041 1301 2146 (AGly)aadA16 0/0 100 99.6 EU675686:3197-4042 (AGly)aadA16 NA
contig00017 99900 101045 (Bla)blaCMY-66 0/0 100 99.4 JN714478:1035-2180 (Bla)blaCMY-66 NA
contig00035 3701 4576 (Bla)blaCTX-M-15 0/0 100 100.0 JQ686199:261-1136 (Bla)blaCTX-M-15 NA
contig00035 19 879 (Bla)blaTEM-105 0/0 100 99.9 AF516720:215-1075 (Bla)blaTEM-105 NA
contig00046 156 836 (Flq)qnrB17 0/0 100 99.8 AM919398:1-681 (Flq)qnrB17 NA
contig00041 2933 3385 (Rif)arr3 0/0 100 100.0 JF806499:1353-1805 (Rif)arr3 NA
contig00041 4 843 (Sul)sul1 0/0 100 100.0 AF071413:6700-7539 (Sul)sul1 NA
contig00037 2675 3490 (Sul)sul2 0/0 100 100.0 EU360945:1617-2432 (Sul)sul2 NA
contig00035 7810 8994 (Tet)tetD 0/0 100 99.9 AB089602:1521-2705 (Tet)tetD NA
contig00041 2327 2800 (Tmt)dfrA27 0/0 100 100.0 EU675686:2543-3016 (Tmt)dfrA27 NA
NCBI
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00041 3482 4036 aac(6’)-Ib-D181Y 0/0 100 99.8 NG_067946.1 AAC(6’)-Ib family aminoglycoside 6’-N-acetyltransferase AMIKACIN, KANAMYCIN, TOBRAMYCIN
contig00041 1301 2146 aadA16 0/0 100 100.0 NG_047339.1 ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA16 STREPTOMYCIN
contig00041 2933 3385 arr-3 0/0 100 100.0 NG_048581.1 NAD(+)–rifampin ADP-ribosyltransferase Arr-3 RIFAMYCIN
contig00017 99900 101045 blaCMY-97 0/0 100 99.8 NG_048894.1 class C beta-lactamase CMY-97 CEPHALOSPORIN
contig00035 3701 4576 blaCTX-M-15 0/0 100 100.0 NG_048935.1 class A extended-spectrum beta-lactamase CTX-M-15 CEPHALOSPORIN
contig00035 19 879 blaTEM-1 0/0 100 100.0 NG_050145.1 class A broad-spectrum beta-lactamase TEM-1 BETA-LACTAM
contig00041 2327 2800 dfrA27 0/0 100 100.0 NG_047723.1 trimethoprim-resistant dihydrofolate reductase DfrA27 TRIMETHOPRIM
contig00046 192 836 qnrB6 0/0 100 99.8 NG_050523.1 quinolone resistance pentapeptide repeat protein QnrB6 QUINOLONE
contig00041 4 843 sul1 0/0 100 100.0 NG_048082.1 sulfonamide-resistant dihydropteroate synthase Sul1 SULFONAMIDE
contig00037 2675 3490 sul2 0/0 100 100.0 NG_051852.1 sulfonamide-resistant dihydropteroate synthase Sul2 SULFONAMIDE
contig00035 7810 8994 tet(D) 0/0 100 99.8 NG_048184.1 tetracycline efflux MFS transporter Tet(D) TETRACYCLINE
MEGARES
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00041 3482 4036 aac(6’)-Ib-D181Y 0/0 100 99.8 NG_067946.1 AAC(6’)-Ib family aminoglycoside 6’-N-acetyltransferase AMIKACIN, KANAMYCIN, TOBRAMYCIN
contig00041 1301 2146 aadA16 0/0 100 100.0 NG_047339.1 ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA16 STREPTOMYCIN
contig00041 2933 3385 arr-3 0/0 100 100.0 NG_048581.1 NAD(+)–rifampin ADP-ribosyltransferase Arr-3 RIFAMYCIN
contig00017 99900 101045 blaCMY-97 0/0 100 99.8 NG_048894.1 class C beta-lactamase CMY-97 CEPHALOSPORIN
contig00035 3701 4576 blaCTX-M-15 0/0 100 100.0 NG_048935.1 class A extended-spectrum beta-lactamase CTX-M-15 CEPHALOSPORIN
contig00035 19 879 blaTEM-1 0/0 100 100.0 NG_050145.1 class A broad-spectrum beta-lactamase TEM-1 BETA-LACTAM
contig00041 2327 2800 dfrA27 0/0 100 100.0 NG_047723.1 trimethoprim-resistant dihydrofolate reductase DfrA27 TRIMETHOPRIM
contig00046 192 836 qnrB6 0/0 100 99.8 NG_050523.1 quinolone resistance pentapeptide repeat protein QnrB6 QUINOLONE
contig00041 4 843 sul1 0/0 100 100.0 NG_048082.1 sulfonamide-resistant dihydropteroate synthase Sul1 SULFONAMIDE
contig00037 2675 3490 sul2 0/0 100 100.0 NG_051852.1 sulfonamide-resistant dihydropteroate synthase Sul2 SULFONAMIDE
contig00035 7810 8994 tet(D) 0/0 100 99.8 NG_048184.1 tetracycline efflux MFS transporter Tet(D) TETRACYCLINE
ORTHO013EII
Resfinder
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00899 1696 2556 aac(3)-IIa_1 0/0 100.0 99.8 X51534 aac(3)-IIa Gentamicin, Tobramycin
contig01080 1539 2138 aac(6’)-Ib-cr_1 0/0 100.0 100.0 DQ303918 aac(6’)-Ib-cr Ciprofloxacin
contig01058 1408 2211 aph(3’’)-Ib_5 0/0 100.0 100.0 AF321551 aph(3’’)-Ib Streptomycin
contig01058 572 1408 aph(6)-Id_1 0/0 100.0 100.0 M28829 aph(6)-Id Streptomycin
contig00346 2798 3936 blaACT-16_1 0/0 99.9 99.5 AB737978 blaACT-16
contig00047 3060 4205 blaACT-6_1 0/0 100.0 91.9 FJ237366 blaACT-6
contig00230 2634 3509 blaCTX-M-15_1 0/0 100.0 100.0 AY044436 blaCTX-M-15 Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig01080 578 1408 blaOXA-1_1 0/0 100.0 100.0 HQ170510 blaOXA-1 Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Piperacillin, Piperacillin+Tazobactam
contig00012 2816 3676 blaTEM-1A_1 0/0 100.0 100.0 HM749966 blaTEM-1A Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig01588 89 730 catA2_1 0/0 100.0 96.1 X53796 catA2 Chloramphenicol
contig02077 445 927 dfrA14_5 0/0 100.0 99.6 DQ388123 dfrA14 Trimethoprim
contig00515 2666 3139 dfrA15_2 0/0 100.0 100.0 AF221900 dfrA15 Trimethoprim
contig01687 1 642 qnrB1_1 0/0 99.5 100.0 DQ351241 qnrB1 Ciprofloxacin
contig00515 429 1295 sul1_5 0/0 100.0 99.8 EU780013 sul1 Sulfamethoxazole
CARD
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00899 1696 2556 AAC(3)-IIe 0/0 100.0 99.5 EU022315.1:0-861 AAC(3)-IIe is a plasmid-encoded aminoglycoside acetyltransferase in E. coli aminoglycoside
contig01080 1539 2138 AAC(6’)-Ib-cr 0/0 100.0 100.0 DQ303918:0-600 AAC(6’)-Ib-cr is an aminoglycoside acetyltransferase encoded by plasmids transposons integrons in Enterobacteriaceae. The aac(6’)-Ib-cr variant gene can induce resistance against aminoglycoside and fluoroquinolone simultaneously aminoglycoside, fluoroquinolone
contig00346 2791 3936 ACT-25 0/0 100.0 99.3 KJ207208:539-1685 ACT-25 is a beta-lactamase. From the Lahey list of ACT beta-lactamases. carbapenem, cephalosporin, cephamycin, penam
contig00047 3060 4205 ACT-6 0/0 100.0 91.9 FJ237366:40-1186 ACT-6 is a beta-lactamase found in Klebsiella pneumoniae carbapenem, cephalosporin, cephamycin, penam
contig01058 1408 2211 APH(3’’)-Ib 0/0 100.0 99.8 AF313472:15593-16397 APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp. aminoglycoside
contig01058 572 1408 APH(6)-Id 0/0 100.0 99.9 AF024602:3155-3992 APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum aminoglycoside
contig01588 89 730 catII_from_Escherichia_coli_K-12 0/0 100.0 96.1 X53796.1:186-828 catII is a chloramphenicol acetyltransferase. This particular catII is found in E.coli K-12. Confers resistance to chloramphenicol. phenicol
contig00230 2634 3509 CTX-M-15 0/0 100.0 100.0 AY044436:1435-2311 CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family cephalosporin
contig02077 445 927 dfrA14 0/0 100.0 99.8 EU780012:2162-2645 dfrA14 is an integron-encoded dihydrofolate reductase found in Escherichia coli diaminopyrimidine
contig00515 2666 3139 dfrA15 0/0 100.0 100.0 KF534911:39-513 dfrA15 is an integron-encoded dihydrofolate reductase found in Vibrio cholerae diaminopyrimidine
contig00120 6170 7363 Enterobacter_cloacae_acrA 0/0 100.0 94.0 DQ679966:299-1493 AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. cloacae. cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig01080 578 1408 OXA-1 0/0 100.0 100.0 JN420336.1:2230-1399 OXA-1 is a beta-lactamase found in E. coli cephalosporin, penam
contig01687 1 642 QnrB1 0/0 99.5 100.0 DQ351241.1:36-681 QnrB1 is a plasmid-mediated quinolone resistance protein found in Klebsiella pneumoniae fluoroquinolone
contig00231 4020 4371 ramA 0/0 93.9 90.9 JQ727668:0-375 RamA (resistance antibiotic multiple) is a positive regulator of AcrAB-TolC and leads to high level multidrug resistance in Klebsiella pneumoniae Salmonella enterica and Enterobacter aerugenes increasing the expression of both the mar operon as well as AcrAB. RamA also decreases OmpF expression. carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00515 429 1268 sul1 0/0 100.0 99.9 JF969163:1053-1893 Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons. sulfonamide
contig00012 2816 3676 TEM-150 0/0 100.0 99.9 AM183304:208-1069 TEM-150 is a beta-lactamase found in Enterobacter spp. E. coli and Klebsiella pneumoniae. cephalosporin, monobactam, penam, penem
ARG-ANNOT
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00899 1696 2556 (AGly)aac3-IIa 0/0 100.0 99.8 X51534:91-951 (AGly)aac3-IIa NA
contig00515 1773 2574 (AGly)aadA1-pm 0/0 96.5 99.9 JQ690540:7968-8798 (AGly)aadA1-pm NA
contig01058 1408 2211 (AGly)strA 0/0 100.0 99.9 AB366441:22458-23261 (AGly)strA NA
contig01058 572 1408 (AGly)strB 0/0 100.0 100.0 FJ474091:264-1100 (AGly)strB NA
contig00346 2791 3936 (Bla)blaACT-16 0/0 100.0 99.1 :NG_050702 (Bla)blaACT-16 NA
contig00047 3060 4205 (Bla)blaACT-6 0/0 100.0 91.9 FJ237366:41-1186 (Bla)blaACT-6 NA
contig00230 2634 3509 (Bla)blaCTX-M-15 0/0 100.0 100.0 JQ686199:261-1136 (Bla)blaCTX-M-15 NA
contig01080 578 1408 (Bla)blaOXA-1 0/0 100.0 100.0 JQ682867:1-831 (Bla)blaOXA-1 NA
contig00012 2816 3676 (Bla)blaTEM-150 0/0 100.0 99.9 AM183304:209-1069 (Bla)blaTEM-150 NA
contig01687 1 642 (Flq)qnrB1 0/0 94.3 100.0 DQ351241:1-681 (Flq)qnrB1 NA
contig01588 89 730 (Phe)catA2 0/0 100.0 96.1 X53796:187-903 (Phe)catA2 NA
contig00515 429 1268 (Sul)sul1 0/0 100.0 99.9 AF071413:6700-7539 (Sul)sul1 NA
contig02077 445 918 (Tmt)dfrA14 0/0 100.0 100.0 GU726917:72-545 (Tmt)dfrA14 NA
contig00515 2666 3139 (Tmt)dfrA15b 0/0 100.0 99.2 AJ867237:177-650 (Tmt)dfrA15b NA
NCBI
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00899 1696 2556 aac(3)-IIe 0/0 100.0 99.8 NG_047244.1 aminoglycoside N-acetyltransferase AAC(3)-IIe GENTAMICIN
contig01080 1539 2093 aac(6’)-Ib-D181Y 0/0 100.0 99.8 NG_067946.1 AAC(6’)-Ib family aminoglycoside 6’-N-acetyltransferase AMIKACIN, KANAMYCIN, TOBRAMYCIN
contig00515 1773 2564 aadA1 0/0 100.0 99.9 NG_052266.1 ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA1 STREPTOMYCIN
contig01058 1408 2235 aph(3’’)-Ib 0/0 100.0 100.0 NG_056002.2 aminoglycoside O-phosphotransferase APH(3’’)-Ib STREPTOMYCIN
contig01058 572 1408 aph(6)-Id 0/0 100.0 100.0 NG_047464.1 aminoglycoside O-phosphotransferase APH(6)-Id STREPTOMYCIN
contig00346 2791 3936 blaACT-45 0/0 100.0 100.0 NG_050708.1 cephalosporin-hydrolyzing class C beta-lactamase ACT-45 CEPHALOSPORIN
contig00047 3060 4205 blaACT-63 0/0 100.0 99.4 NG_061406.1 cephalosporin-hydrolyzing class C beta-lactamase ACT-63 CEPHALOSPORIN
contig00230 2634 3509 blaCTX-M-15 0/0 100.0 100.0 NG_048935.1 class A extended-spectrum beta-lactamase CTX-M-15 CEPHALOSPORIN
contig01080 578 1408 blaOXA-1 0/0 100.0 100.0 NG_049392.1 oxacillin-hydrolyzing class D beta-lactamase OXA-1 CEPHALOSPORIN
contig00012 2816 3676 blaTEM-150 0/0 100.0 99.9 NG_050194.1 class A beta-lactamase TEM-150 BETA-LACTAM
contig01588 89 730 catA2 0/0 100.0 100.0 NG_047596.1 type A-2 chloramphenicol O-acetyltransferase CatII CHLORAMPHENICOL
contig02077 445 918 dfrA14 0/0 100.0 100.0 NG_056035.1 trimethoprim-resistant dihydrofolate reductase DfrA14 TRIMETHOPRIM
contig00515 2666 3139 dfrA15 0/0 100.0 100.0 NG_047702.1 trimethoprim-resistant dihydrofolate reductase DfrA15 TRIMETHOPRIM
contig01687 1 642 qnrB1 0/0 99.5 100.0 NG_050469.1 quinolone resistance pentapeptide repeat protein QnrB1 QUINOLONE
contig00515 429 1268 sul1 0/0 100.0 99.9 NG_048082.1 sulfonamide-resistant dihydropteroate synthase Sul1 SULFONAMIDE
MEGARES
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00899 1696 2556 aac(3)-IIe 0/0 100.0 99.8 NG_047244.1 aminoglycoside N-acetyltransferase AAC(3)-IIe GENTAMICIN
contig01080 1539 2093 aac(6’)-Ib-D181Y 0/0 100.0 99.8 NG_067946.1 AAC(6’)-Ib family aminoglycoside 6’-N-acetyltransferase AMIKACIN, KANAMYCIN, TOBRAMYCIN
contig00515 1773 2564 aadA1 0/0 100.0 99.9 NG_052266.1 ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA1 STREPTOMYCIN
contig01058 1408 2235 aph(3’’)-Ib 0/0 100.0 100.0 NG_056002.2 aminoglycoside O-phosphotransferase APH(3’’)-Ib STREPTOMYCIN
contig01058 572 1408 aph(6)-Id 0/0 100.0 100.0 NG_047464.1 aminoglycoside O-phosphotransferase APH(6)-Id STREPTOMYCIN
contig00346 2791 3936 blaACT-45 0/0 100.0 100.0 NG_050708.1 cephalosporin-hydrolyzing class C beta-lactamase ACT-45 CEPHALOSPORIN
contig00047 3060 4205 blaACT-63 0/0 100.0 99.4 NG_061406.1 cephalosporin-hydrolyzing class C beta-lactamase ACT-63 CEPHALOSPORIN
contig00230 2634 3509 blaCTX-M-15 0/0 100.0 100.0 NG_048935.1 class A extended-spectrum beta-lactamase CTX-M-15 CEPHALOSPORIN
contig01080 578 1408 blaOXA-1 0/0 100.0 100.0 NG_049392.1 oxacillin-hydrolyzing class D beta-lactamase OXA-1 CEPHALOSPORIN
contig00012 2816 3676 blaTEM-150 0/0 100.0 99.9 NG_050194.1 class A beta-lactamase TEM-150 BETA-LACTAM
contig01588 89 730 catA2 0/0 100.0 100.0 NG_047596.1 type A-2 chloramphenicol O-acetyltransferase CatII CHLORAMPHENICOL
contig02077 445 918 dfrA14 0/0 100.0 100.0 NG_056035.1 trimethoprim-resistant dihydrofolate reductase DfrA14 TRIMETHOPRIM
contig00515 2666 3139 dfrA15 0/0 100.0 100.0 NG_047702.1 trimethoprim-resistant dihydrofolate reductase DfrA15 TRIMETHOPRIM
contig01687 1 642 qnrB1 0/0 99.5 100.0 NG_050469.1 quinolone resistance pentapeptide repeat protein QnrB1 QUINOLONE
contig00515 429 1268 sul1 0/0 100.0 99.9 NG_048082.1 sulfonamide-resistant dihydropteroate synthase Sul1 SULFONAMIDE
ORTHO039E
Resfinder
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00082 1696 2556 aac(3)-IIa_1 0/0 100.0 99.8 X51534 aac(3)-IIa Gentamicin, Tobramycin
contig00084 1539 2138 aac(6’)-Ib-cr_1 0/0 100.0 100.0 DQ303918 aac(6’)-Ib-cr Ciprofloxacin
contig00092 126 1090 ant(3’’)-Ia_1 3/7 99.3 99.1 X02340 ant(3’’)-Ia Streptomycin
contig00067 3533 4336 aph(3’’)-Ib_5 0/0 100.0 100.0 AF321551 aph(3’’)-Ib Streptomycin
contig00067 2697 3533 aph(6)-Id_1 0/0 100.0 100.0 M28829 aph(6)-Id Streptomycin
contig00006 95444 96589 blaACT-7_1 0/0 100.0 99.6 FJ237368 blaACT-7
contig00076 2636 3511 blaCTX-M-15_1 0/0 100.0 100.0 AY044436 blaCTX-M-15 Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00084 578 1408 blaOXA-1_1 0/0 100.0 100.0 HQ170510 blaOXA-1 Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Piperacillin, Piperacillin+Tazobactam
contig00067 1116 1976 blaTEM-1B_1 0/0 100.0 100.0 AY458016 blaTEM-1B Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00087 350 1004 catA1_1 0/0 99.2 99.8 V00622 catA1 Chloramphenicol
contig00065 5401 5883 dfrA14_5 0/0 100.0 99.6 DQ388123 dfrA14 Trimethoprim
contig00058 9456 9881 fosA_1 0/0 100.0 96.5 M85195 fosA Fosfomycin
contig00066 4405 5049 qnrB1_1 0/0 100.0 100.0 DQ351241 qnrB1 Ciprofloxacin
contig00067 4397 5212 sul2_2 0/0 100.0 100.0 AY034138 sul2 Sulfamethoxazole
contig00075 1429 2697 tet(A)_6 1/22 97.8 93.2 AF534183 tet(A) Doxycycline, Tetracycline
CARD
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00082 1696 2556 AAC(3)-IIe 0/0 100.0 99.5 EU022315.1:0-861 AAC(3)-IIe is a plasmid-encoded aminoglycoside acetyltransferase in E. coli aminoglycoside
contig00084 1539 2138 AAC(6’)-Ib-cr 0/0 100.0 100.0 DQ303918:0-600 AAC(6’)-Ib-cr is an aminoglycoside acetyltransferase encoded by plasmids transposons integrons in Enterobacteriaceae. The aac(6’)-Ib-cr variant gene can induce resistance against aminoglycoside and fluoroquinolone simultaneously aminoglycoside, fluoroquinolone
contig00006 95444 96589 ACT-17 0/0 100.0 99.6 KF992026:753-1899 ACT-17 is a beta-lactamase. From the Lahey list of ACT beta-lactamases. carbapenem, cephalosporin, cephamycin, penam
contig00092 126 1090 ANT(3’’)-IIa 3/7 99.3 99.1 X02340.1:222-1194 ANT(3’’)-IIa is a aminoglycoside nucleotidyltransferase identified in Acinetobacter spp. via horizontal gene transfer mechanisms. aminoglycoside
contig00067 3533 4336 APH(3’’)-Ib 0/0 100.0 99.8 AF313472:15593-16397 APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp. aminoglycoside
contig00067 2697 3533 APH(6)-Id 0/0 100.0 99.9 AF024602:3155-3992 APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum aminoglycoside
contig00087 350 1004 catI 0/0 99.2 99.8 V00622:243-903 catI is a chromosome and transposon-encoded variant of the cat gene found in Escherichia coli and Acinetobacter baumannii phenicol
contig00076 2636 3511 CTX-M-15 0/0 100.0 100.0 AY044436:1435-2311 CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family cephalosporin
contig00065 5401 5883 dfrA14 0/0 100.0 99.8 EU780012:2162-2645 dfrA14 is an integron-encoded dihydrofolate reductase found in Escherichia coli diaminopyrimidine
contig00058 9456 9881 FosA2 0/0 100.0 92.7 EU487198:216-642 An enzyme that confers resistance to fosfomycin in Enterobacter cloacae by breaking the epoxide ring of the molecule. It depends on the cofactors Manganese (II) and Potassium and uses Glutathione (GSH) as the nucleophilic molecule. fosfomycin
contig00084 578 1408 OXA-1 0/0 100.0 100.0 JN420336.1:2230-1399 OXA-1 is a beta-lactamase found in E. coli cephalosporin, penam
contig00066 4368 5049 QnrB17 1/1 100.0 99.1 AM919398:0-681 QnrB17 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii fluoroquinolone
contig00067 4397 5212 sul2 0/0 100.0 100.0 AY055428.1:21084-20268 Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids. sulfonamide
contig00067 1116 1976 TEM-1 0/0 100.0 99.9 AL513383:161910-162771 TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins. cephalosporin, monobactam, penam, penem
contig00075 1429 2697 tet(A) 1/22 97.8 93.2 AF534183.1:2970-4245 TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria. tetracycline
ARG-ANNOT
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00082 1696 2556 (AGly)aac3-IIa 0/0 100.0 99.8 X51534:91-951 (AGly)aac3-IIa NA
contig00092 126 937 (AGly)aadA1-pm 0/0 97.7 99.9 JQ690540:7968-8798 (AGly)aadA1-pm NA
contig00067 3533 4336 (AGly)strA 0/0 100.0 99.9 AB366441:22458-23261 (AGly)strA NA
contig00067 2697 3533 (AGly)strB 0/0 100.0 100.0 FJ474091:264-1100 (AGly)strB NA
contig00006 95444 96589 (Bla)blaACT-7 0/0 100.0 99.6 FJ237368:1-1146 (Bla)blaACT-7 NA
contig00076 2636 3511 (Bla)blaCTX-M-15 0/0 100.0 100.0 JQ686199:261-1136 (Bla)blaCTX-M-15 NA
contig00084 578 1408 (Bla)blaOXA-1 0/0 100.0 100.0 JQ682867:1-831 (Bla)blaOXA-1 NA
contig00067 1116 1976 (Bla)blaTEM-105 0/0 100.0 99.9 AF516720:215-1075 (Bla)blaTEM-105 NA
contig00058 9456 9881 (Fcyn)FosA2 0/0 100.0 92.7 EU487198:217-642 (Fcyn)FosA2 NA
contig00066 4368 5049 (Flq)qnrB1 1/1 100.0 99.8 DQ351241:1-681 (Flq)qnrB1 NA
contig00087 350 1004 (Phe)catA1 0/0 99.2 99.8 V00622:244-903 (Phe)catA1 NA
contig00067 4397 5212 (Sul)sul2 0/0 100.0 100.0 EU360945:1617-2432 (Sul)sul2 NA
contig00075 1429 2725 (Tet)tetA 1/22 100.0 93.3 JX424423:94438-95712 (Tet)tetA NA
contig00075 757 1398 (Tet)tetR 1/9 98.6 93.1 HF545434:53576-54226 (Tet)tetR NA
contig00065 5401 5874 (Tmt)dfrA14 0/0 100.0 100.0 GU726917:72-545 (Tmt)dfrA14 NA
NCBI
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00082 1696 2556 aac(3)-IIe 0/0 100.0 99.8 NG_047244.1 aminoglycoside N-acetyltransferase AAC(3)-IIe GENTAMICIN
contig00084 1539 2093 aac(6’)-Ib-D181Y 0/0 100.0 99.8 NG_067946.1 AAC(6’)-Ib family aminoglycoside 6’-N-acetyltransferase AMIKACIN, KANAMYCIN, TOBRAMYCIN
contig00092 126 917 aadA1 0/0 100.0 100.0 NG_052536.1 ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA1 STREPTOMYCIN
contig00067 3533 4360 aph(3’’)-Ib 0/0 100.0 100.0 NG_056002.2 aminoglycoside O-phosphotransferase APH(3’’)-Ib STREPTOMYCIN
contig00067 2697 3533 aph(6)-Id 0/0 100.0 100.0 NG_047464.1 aminoglycoside O-phosphotransferase APH(6)-Id STREPTOMYCIN
contig00006 95444 96589 blaACT-40 0/0 100.0 100.0 NG_050703.1 cephalosporin-hydrolyzing class C beta-lactamase ACT-40 CEPHALOSPORIN
contig00076 2636 3511 blaCTX-M-15 0/0 100.0 100.0 NG_048935.1 class A extended-spectrum beta-lactamase CTX-M-15 CEPHALOSPORIN
contig00084 578 1408 blaOXA-1 0/0 100.0 100.0 NG_049392.1 oxacillin-hydrolyzing class D beta-lactamase OXA-1 CEPHALOSPORIN
contig00067 1116 1976 blaTEM-1 0/0 100.0 100.0 NG_050145.1 class A broad-spectrum beta-lactamase TEM-1 BETA-LACTAM
contig00087 350 1004 catA1 0/0 99.2 99.8 NG_047582.1 type A-1 chloramphenicol O-acetyltransferase CHLORAMPHENICOL
contig00065 5401 5874 dfrA14 0/0 100.0 100.0 NG_056035.1 trimethoprim-resistant dihydrofolate reductase DfrA14 TRIMETHOPRIM
contig00058 9456 9881 fosA 0/0 100.0 96.5 NG_050405.1 fosfomycin resistance glutathione transferase FosA FOSFOMYCIN
contig00066 4405 5049 qnrB1 0/0 100.0 100.0 NG_050469.1 quinolone resistance pentapeptide repeat protein QnrB1 QUINOLONE
contig00067 4397 5212 sul2 0/0 100.0 100.0 NG_051852.1 sulfonamide-resistant dihydropteroate synthase Sul2 SULFONAMIDE
contig00075 1526 2725 tet(A) 0/0 100.0 100.0 NG_048157.1 tetracycline efflux MFS transporter Tet(A) TETRACYCLINE
MEGARES
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00082 1696 2556 aac(3)-IIe 0/0 100.0 99.8 NG_047244.1 aminoglycoside N-acetyltransferase AAC(3)-IIe GENTAMICIN
contig00084 1539 2093 aac(6’)-Ib-D181Y 0/0 100.0 99.8 NG_067946.1 AAC(6’)-Ib family aminoglycoside 6’-N-acetyltransferase AMIKACIN, KANAMYCIN, TOBRAMYCIN
contig00092 126 917 aadA1 0/0 100.0 100.0 NG_052536.1 ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA1 STREPTOMYCIN
contig00067 3533 4360 aph(3’’)-Ib 0/0 100.0 100.0 NG_056002.2 aminoglycoside O-phosphotransferase APH(3’’)-Ib STREPTOMYCIN
contig00067 2697 3533 aph(6)-Id 0/0 100.0 100.0 NG_047464.1 aminoglycoside O-phosphotransferase APH(6)-Id STREPTOMYCIN
contig00006 95444 96589 blaACT-40 0/0 100.0 100.0 NG_050703.1 cephalosporin-hydrolyzing class C beta-lactamase ACT-40 CEPHALOSPORIN
contig00076 2636 3511 blaCTX-M-15 0/0 100.0 100.0 NG_048935.1 class A extended-spectrum beta-lactamase CTX-M-15 CEPHALOSPORIN
contig00084 578 1408 blaOXA-1 0/0 100.0 100.0 NG_049392.1 oxacillin-hydrolyzing class D beta-lactamase OXA-1 CEPHALOSPORIN
contig00067 1116 1976 blaTEM-1 0/0 100.0 100.0 NG_050145.1 class A broad-spectrum beta-lactamase TEM-1 BETA-LACTAM
contig00087 350 1004 catA1 0/0 99.2 99.8 NG_047582.1 type A-1 chloramphenicol O-acetyltransferase CHLORAMPHENICOL
contig00065 5401 5874 dfrA14 0/0 100.0 100.0 NG_056035.1 trimethoprim-resistant dihydrofolate reductase DfrA14 TRIMETHOPRIM
contig00058 9456 9881 fosA 0/0 100.0 96.5 NG_050405.1 fosfomycin resistance glutathione transferase FosA FOSFOMYCIN
contig00066 4405 5049 qnrB1 0/0 100.0 100.0 NG_050469.1 quinolone resistance pentapeptide repeat protein QnrB1 QUINOLONE
contig00067 4397 5212 sul2 0/0 100.0 100.0 NG_051852.1 sulfonamide-resistant dihydropteroate synthase Sul2 SULFONAMIDE
contig00075 1526 2725 tet(A) 0/0 100.0 100.0 NG_048157.1 tetracycline efflux MFS transporter Tet(A) TETRACYCLINE


Summary figures

Presence/Absence of antibiotic resistance genes (coverage and identity > 90%) on each sample

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Resfinder
CARD
ARG-ANNOT
NCBI
MEGARES


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Plasmid Profiling


Field Description
Contig Contig name where the gene was found
Start Start position of the gene within the contig
End End position of the gene within the contig
Gene Antibiotic resistance gene
Gaps Gaps in subject (genome) and query (antibiotic resistance gene)
Coverage Proportion (%) of the gene covered
Identity Proportion (%) of exact nucleotide matches
Accession Accesion number of the antibiotic resistance gene
Product Antibiotic resistance gene product


Select sample

ID084I
Contig Start End Gene Gaps Coverage Identity Accession Product
contig00032 16028 16623 RepA_1_pKPC-CAV1321 0/0 100 100 CP011611 RepA_1_pKPC-CAV1321_CP011611
ORTHO013EII
Contig Start End Gene Gaps Coverage Identity Accession Product
contig00553 1798 2440 IncFIB(pB171)_1_pB171 0/0 100 91.5 AB024946 IncFIB(pB171)_1_pB171_AB024946
contig00213 3438 3997 IncFIB(pECLA)_1_pECLA 0/0 100 100.0 CP001919 IncFIB(pECLA)_1_pECLA_CP001919
contig00226 6578 7324 IncFII(pECLA)_1_pECLA 0/0 100 100.0 CP001919 IncFII(pECLA)_1_pECLA_CP001919
contig00310 3749 3978 IncFII(Yp)_1_Yersenia 0/0 100 99.6 CP000670 IncFII(Yp)_1_Yersenia_CP000670
ORTHO039E
Contig Start End Gene Gaps Coverage Identity Accession Product
contig00042 7952 8698 IncFII(pECLA)_1_pECLA 0/0 100 97.3 CP001919 IncFII(pECLA)_1_pECLA_CP001919
contig00041 28465 28791 IncHI2_1 0/0 100 100.0 BX664015 IncHI2_1__BX664015
contig00019 84375 85004 IncHI2A_1 0/0 100 100.0 BX664015 IncHI2A_1__BX664015


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Virulence Factor Determination


Field Description
Contig Contig name where the gene was found
Start Start position of the gene within the contig
End End position of the gene within the contig
Gene Antibiotic resistance gene
Coverage Proportion (%) of the gene covered
Identity Proportion (%) of exact nucleotide matches
Accession Accesion number of the antibiotic resistance gene
Product Antibiotic resistance gene product


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ID084I
Contig Start End Strand Gene Coverage Identity Accession Product
contig00001 339615 340109 + chuX 100.0 82.2 NP_756177 (chuX) putative heme-binding protein ChuX [Chu (VF0227)] [Escherichia coli CFT073]
contig00006 71670 72128 - csgB 100.0 81.7 NP_460114 (csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00006 72890 73540 + csgD 100.0 83.6 NP_460113 (csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00006 73545 73937 + csgE 99.2 82.8 NP_460112 (csgE) curli production assembly/transport protein CsgE [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00006 73963 74376 + csgF 99.3 81.1 NP_460111 (csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00006 74402 75235 + csgG 99.8 82.3 NP_460110 (csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00001 209564 210421 - entB 100.0 80.7 NP_752613 (entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001 210435 212045 - entE 99.9 81.6 NP_752612 (entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001 217796 218583 + fepC 96.6 81.1 NP_752606 (fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011 141012 141997 + fliG 99.3 80.5 YP_001006742 (fliG) flagellar motor switch protein G [Flagella (VF0394)] [Yersinia enterocolitica subsp. enterocolitica 8081]
contig00006 131252 132310 + ompA 99.5 87.3 AAF37887 (ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
ORTHO013EII
Contig Start End Strand Gene Coverage Identity Accession Product
contig00165 9121 9235 - astA 98.3 91.3 BAA94855 (astA) heat-stable enterotoxin 1 [EAST1 (VF0216)] [Escherichia coli O44:H18 042]
contig00024 1898 2731 - csgG 100.0 81.7 NP_460110 (csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00055 10436 10972 - lpfA 100.0 89.2 NP_462541 (lpfA) long polar fimbria protein LpfA [Lpf (VF0105)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00055 9652 10350 - lpfB 100.0 89.1 NP_462540 (lpfB) long polar fimbrial chaperone protein LpfB [Lpf (VF0105)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00055 7101 9629 - lpfC 100.0 90.1 NP_462539 (lpfC) long polar fimbrial usher protein LpfC [Lpf (VF0105)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00055 5474 6001 - lpfE 100.0 83.3 NP_462537 (lpfE) long polar fimbrial minor subunit LpfE adhesin [Lpf (VF0105)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00133 42 941 + ompA 86.2 84.8 AAF37887 (ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
ORTHO039E
Contig Start End Strand Gene Coverage Identity Accession Product
contig00020 83752 84581 + csgG 99.4 80.8 NP_460110 (csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00024 36938 38100 - iroB 99.9 89.8 NP_753168 (iroB) glucosyltransferase IroB [Salmochelin (IA013)] [Escherichia coli CFT073]
contig00024 33151 36878 - iroC 99.6 89.0 NP_753167 (iroC) ATP binding cassette transporter [Salmochelin (IA013)] [Escherichia coli CFT073]
contig00024 31806 33035 - iroD 100.0 87.8 NP_753166 (iroD) esterase [Salmochelin (IA013)] [Escherichia coli CFT073]
contig00024 30766 31722 - iroE 100.0 86.9 NP_753165 (iroE) esterase [Salmochelin (IA013)] [Escherichia coli CFT073]
contig00024 28547 30721 + iroN 99.9 91.1 NP_753164 (iroN) salmochelin receptor IroN [IroN (VF0230)] [Escherichia coli CFT073]
contig00032 22908 23950 - ompA 99.0 84.7 AAF37887 (ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]


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Multi-Locus Sequence Typing (MLST)


Symbol Meaning
~ novel full length allele similar to match
? partial match to known allele
- allele missing


Scheme ST 1 2 3 4 5 6 7
ID084I cfreundii 263 aspC(16) clpX(30) fadD(33) mdh(28) arcA(5) dnaG(28) lysP(74)
ORTHO013EII ecloacae - dnaA(52) fusA(106) gyrB(20) leuS(44,237) pyrG(45) rplB(12) rpoB(148)
ORTHO039E ecloacae 1015 dnaA(4) fusA(4) gyrB(68) leuS(6) pyrG(39) rplB(4) rpoB(25)

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Pangenome Analysis

Pangenome genes summary

Genes Description Number
Core genes (99% <= strains <= 100%) 343
Soft core genes (95% <= strains < 99%) 0
Shell genes (15% <= strains < 95%) 14102
Cloud genes (0% <= strains < 15%) 0
Total genes (0% <= strains <= 100%) 14445

Schematic representation of genes presence (color) or absence (blank) between samples:


Pangenome tree based on presence/absence of accessory genes representation

Rectangular (phylogram)

Circular (phylogram)

Circular (cladogram)


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Pangenome tree based on core genome alignment representation

Rectangular (phylogram)

Circular (phylogram)

Circular (cladogram)


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Insertion sequence characterization


Field Description
Region Numeric code given to insertion sequence (IS)
Orientation The orientation of IS position: Either forward (F) or reverse (F)
X-cordinates The left coordinate of the position
Y-coordinates The right coordinate of the position
Gap The distance between the x and y coordinates
CallType Describes whether a position hit is novel (not in reference) or known (in the reference)
LeftGene Locus tag ID of the gene closest to the left side of the IS position
LeftGeneDescription Description of the gene feature from the left side of the IS position. By default this is the product position
RightGene Locus tag ID of the gene closest to the right side of the IS position
RightGeneDescription Description of the gene feature from the right side of the IS position. By default this is the product position


Select the sample

ORTHO013EII
Region Orientation X-coordinates Y-coordinates Gap CallType LeftGene LeftGeneDescription RightGene RightGeneDescription
region_1 R -1 2023638 2023639 novel CfB38_4905 50S ribosomal protein L34 CfB38_1939 IS1 insA protein
ORTHO039E
Region Orientation X-coordinates Y-coordinates Gap CallType LeftGene LeftGeneDescription RightGene RightGeneDescription
region_1 R -1 847919 847920 novel CfB38_4905 50S ribosomal protein L34 CfB38_0804 N-glycosyltransferase


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Citations and Bibliography

If you have used rMAP, please cite:

Sserwadda, I., & Mboowa, G. (2021). rMAP: the Rapid Microbial Analysis Pipeline for ESKAPE bacterial group whole-genome sequence data. Microbial genomics, 7(6), 10.1099/mgen.0.000583. https://doi.org/10.1099/mgen.0.000583


The philosophy of rMAP was built on the foundation of already pre-existing tools. As a token of gratitude to the authors of those numerous tools, please also cite:


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